hyperrectangle_deviation_assessment: Calculation of deviation components
In TTMap: Two-Tier Mapper: a clustering tool based on topological data analysis

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/hyperrectangle_deviation_assessment.R

hyperrectangle_deviation_assessment function calculates the hyperrectangle deviation assessment (HDA) that calculates the deviation components using normal_hda2 which calculates the normal component of the test sample and deviation_hda2 which calculates the deviation component.

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    hyperrectangle_deviation_assessment(x, 
    k = dim(x$Normal.mat)[2], dataname, 
    normalname,Org.directory = getwd())

`x`	output object given back by `control_adjustment`, list
`k`	A factor if not all the lines in the control group should be kept
`dataname`	the name of the project
`normalname`	A name for the corrected control files
`Org.directory`	where the outputs should be saved

The function performs the hyperrectangle deviation assessment (HDA)

Outputs

`Tdis.pcl`	The matrix of the deviation components for each test sample
`Tnorm.pcl`	The matrix of the normal components for each test sample
`NormalModel.pcl`	The normal model used

Values

`Dc.Dmat`	the deviation component matrix composed of the deviation components of all the samples in the test group
`m`	the values of the filter function per sample in the test group

Rachel Jeitziner

control_adjustment, hyperrectangle_deviation_assessment, ttmap_sgn_genes

    ##a full example can be found in ttmap_sgn_genes
    ##--
    library(airway)
    data(airway)
    airway <- airway[rowSums(assay(airway))>80,]
    assay(airway) <- log(assay(airway)+1,2)
    ALPHA <- 1
    the_experiment <- TTMap::make_matrices(airway,
    seq_len(4), seq_len(4) + 4,
    rownames(airway), rownames(airway))
    TTMAP_part1prime <-TTMap::control_adjustment(
    normal.pcl = the_experiment$CTRL,
    tumor.pcl = the_experiment$TEST, 
    normalname = "The_healthy_controls", 
    dataname = "Effect_of_cancer", 
    org.directory = tempdir(), e = 0, P = 1.1, B = 0);
    Kprime <- 4;
    TTMAP_part1_hda <-
    TTMap::hyperrectangle_deviation_assessment(x = 
    TTMAP_part1prime,
    k = Kprime, dataname = "Effect_of_cancer",
    normalname = "The_healthy_controls");